/* -*- mode: c; tab-width: 4; indent-tabs-mode: nil; c-basic-offset: 4; c-file-style: "stroustrup"; -*-
 *
 * 
 *                This source code is part of
 * 
 *                 G   R   O   M   A   C   S
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 *          GROningen MAchine for Chemical Simulations
 * 
 *                        VERSION 3.2.0
 * Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
 * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
 * Copyright (c) 2001-2004, The GROMACS development team,
 * check out http://www.gromacs.org for more information.

 * This program is free software; you can redistribute it and/or
 * modify it under the terms of the GNU General Public License
 * as published by the Free Software Foundation; either version 2
 * of the License, or (at your option) any later version.
 * 
 * If you want to redistribute modifications, please consider that
 * scientific software is very special. Version control is crucial -
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 */
#ifdef HAVE_CONFIG_H
#include <config.h>
#endif

#include <math.h>
#include <string.h>
#include <ctype.h>
#include "pdbio.h"
#include "confio.h"
#include "symtab.h"
#include "smalloc.h"
#include "macros.h"
#include "copyrite.h"
#include "statutil.h"
#include "string2.h"
#include "strdb.h"
#include "index.h"
#include "vec.h"
#include "typedefs.h"
#include "gbutil.h"
#include "strdb.h"
#include "physics.h"
#include "atomprop.h"
#include "tpxio.h"
#include "pbc.h"
#include "princ.h"
#include "txtdump.h"
#include "viewit.h"
#include "rmpbc.h"
#include "gmx_ana.h"

typedef struct
{
    char sanm[12];
    int natm;
    int nw;
    char anm[6][12];
} t_simat;

typedef struct
{
    char reso[12];
    char resn[12];
    int nsatm;
    t_simat sat[3];
} t_simlist;
static const char *pdbtp[epdbNR] =
    { "ATOM  ", "HETATM" };

real calc_mass(t_atoms *atoms, gmx_bool bGetMass, gmx_atomprop_t aps)
{
    real tmass;
    int i;

    tmass = 0;
    for (i = 0; (i < atoms->nr); i++)
    {
        if (bGetMass)
        {
            gmx_atomprop_query(aps, epropMass,
                               *atoms->resinfo[atoms->atom[i].resind].name,
                               *atoms->atomname[i], &(atoms->atom[i].m));
        }
        tmass += atoms->atom[i].m;
    }

    return tmass;
}

real calc_geom(int isize, atom_id *index, rvec *x, rvec geom_center, rvec min,
               rvec max, gmx_bool bDiam)
{
    real diam2, d;
    char *grpnames;
    int ii, i, j;

    clear_rvec(geom_center);
    diam2 = 0;
    if (isize == 0)
    {
        clear_rvec(min);
        clear_rvec(max);
    }
    else
    {
        if (index)
            ii = index[0];
        else
            ii = 0;
        for (j = 0; j < DIM; j++)
            min[j] = max[j] = x[ii][j];
        for (i = 0; i < isize; i++)
        {
            if (index)
                ii = index[i];
            else
                ii = i;
            rvec_inc(geom_center, x[ii]);
            for (j = 0; j < DIM; j++)
            {
                if (x[ii][j] < min[j])
                    min[j] = x[ii][j];
                if (x[ii][j] > max[j])
                    max[j] = x[ii][j];
            }
            if (bDiam)
            {
                if (index)
                    for (j = i + 1; j < isize; j++)
                    {
                        d = distance2(x[ii], x[index[j]]);
                        diam2 = max(d,diam2);
                    }
                else
                    for (j = i + 1; j < isize; j++)
                    {
                        d = distance2(x[i], x[j]);
                        diam2 = max(d,diam2);
                    }
            }
        }
        svmul(1.0 / isize, geom_center, geom_center);
    }

    return sqrt(diam2);
}

void center_conf(int natom, rvec *x, rvec center, rvec geom_cent)
{
    int i;
    rvec shift;

    rvec_sub(center, geom_cent, shift);

    printf("    shift       :%7.3f%7.3f%7.3f (nm)\n", shift[XX], shift[YY],
           shift[ZZ]);

    for (i = 0; (i < natom); i++)
        rvec_inc(x[i], shift);
}

void scale_conf(int natom, rvec x[], matrix box, rvec scale)
{
    int i, j;

    for (i = 0; i < natom; i++)
    {
        for (j = 0; j < DIM; j++)
            x[i][j] *= scale[j];
    }
    for (i = 0; i < DIM; i++)
        for (j = 0; j < DIM; j++)
            box[i][j] *= scale[j];
}

void read_bfac(const char *fn, int *n_bfac, double **bfac_val, int **bfac_nr)
{
    int i;
    char **bfac_lines;

    *n_bfac = get_lines(fn, &bfac_lines);
    snew(*bfac_val, *n_bfac);
    snew(*bfac_nr, *n_bfac);
    fprintf(stderr, "Reading %d B-factors from %s\n", *n_bfac, fn);
    for (i = 0; (i < *n_bfac); i++)
    {
        /*fprintf(stderr, "Line %d: %s",i,bfac_lines[i]);*/
        sscanf(bfac_lines[i], "%d %lf", &(*bfac_nr)[i], &(*bfac_val)[i]);
        /*fprintf(stderr," nr %d val %g\n",(*bfac_nr)[i],(*bfac_val)[i]);*/
    }

}

void set_pdb_conf_bfac(int natoms, int nres, t_atoms *atoms, int n_bfac,
                       double *bfac, int *bfac_nr, gmx_bool peratom)
{
    FILE *out;
    real bfac_min, bfac_max;
    int i, n;
    gmx_bool found;

    bfac_max = -1e10;
    bfac_min = 1e10;
    for (i = 0; (i < n_bfac); i++)
    {
        if (bfac_nr[i] - 1 >= atoms->nres)
            peratom = TRUE;
        /*    if ((bfac_nr[i]-1<0) || (bfac_nr[i]-1>=atoms->nr))
         gmx_fatal(FARGS,"Index of B-Factor %d is out of range: %d (%g)",
         i+1,bfac_nr[i],bfac[i]); */
        if (bfac[i] > bfac_max)
            bfac_max = bfac[i];
        if (bfac[i] < bfac_min)
            bfac_min = bfac[i];
    }
    while ((bfac_max > 99.99) || (bfac_min < -99.99))
    {
        fprintf(stderr,
                "Range of values for B-factors too large (min %g, max %g) "
                    "will scale down a factor 10\n", bfac_min, bfac_max);
        for (i = 0; (i < n_bfac); i++)
            bfac[i] /= 10;
        bfac_max /= 10;
        bfac_min /= 10;
    }
    while ((fabs(bfac_max) < 0.5) && (fabs(bfac_min) < 0.5))
    {
        fprintf(stderr,
                "Range of values for B-factors too small (min %g, max %g) "
                    "will scale up a factor 10\n", bfac_min, bfac_max);
        for (i = 0; (i < n_bfac); i++)
            bfac[i] *= 10;
        bfac_max *= 10;
        bfac_min *= 10;
    }

    for (i = 0; (i < natoms); i++)
        atoms->pdbinfo[i].bfac = 0;

    if (!peratom)
    {
        fprintf(stderr, "Will attach %d B-factors to %d residues\n", n_bfac,
                nres);
        for (i = 0; (i < n_bfac); i++)
        {
            found = FALSE;
            for (n = 0; (n < natoms); n++)
                if (bfac_nr[i] == atoms->resinfo[atoms->atom[n].resind].nr)
                {
                    atoms->pdbinfo[n].bfac = bfac[i];
                    found = TRUE;
                }
            if (!found)
            {
                gmx_warning("Residue nr %d not found\n", bfac_nr[i]);
            }
        }
    }
    else
    {
        fprintf(stderr, "Will attach %d B-factors to %d atoms\n", n_bfac,
                natoms);
        for (i = 0; (i < n_bfac); i++)
        {
            atoms->pdbinfo[bfac_nr[i] - 1].bfac = bfac[i];
        }
    }
}

void pdb_legend(FILE *out, int natoms, int nres, t_atoms *atoms, rvec x[])
{
    real bfac_min, bfac_max, xmin, ymin, zmin;
    int i;
    int space = ' ';

    bfac_max = -1e10;
    bfac_min = 1e10;
    xmin = 1e10;
    ymin = 1e10;
    zmin = 1e10;
    for (i = 0; (i < natoms); i++)
    {
        xmin = min(xmin,x[i][XX]);
        ymin = min(ymin,x[i][YY]);
        zmin = min(zmin,x[i][ZZ]);
        bfac_min = min(bfac_min,atoms->pdbinfo[i].bfac);
        bfac_max = max(bfac_max,atoms->pdbinfo[i].bfac);
    }
    fprintf(stderr, "B-factors range from %g to %g\n", bfac_min, bfac_max);
    for (i = 1; (i < 12); i++)
    {
        fprintf(out,
                "%-6s%5u  %-4.4s%3.3s %c%4d%c   %8.3f%8.3f%8.3f%6.2f%6.2f\n",
                "ATOM  ", natoms + 1 + i, "CA", "LEG", space, nres + 1, space,
                (xmin + (i * 0.12)) * 10, ymin * 10, zmin * 10, 1.0, bfac_min
                    + ((i - 1.0) * (bfac_max - bfac_min) / 10));
    }
}

void visualize_images(const char *fn, int ePBC, matrix box)
{
    t_atoms atoms;
    rvec *img;
    char *c, *ala;
    int nat, i;

    nat = NTRICIMG + 1;
    init_t_atoms(&atoms, nat, FALSE);
    atoms.nr = nat;
    snew(img,nat);
    /* FIXME: Constness should not be cast away */
    c = (char *) "C";
    ala = (char *) "ALA";
    for (i = 0; i < nat; i++)
    {
        atoms.atomname[i] = &c;
        atoms.atom[i].resind = i;
        atoms.resinfo[i].name = &ala;
        atoms.resinfo[i].nr = i + 1;
        atoms.resinfo[i].chainid = 'A' + i / NCUCVERT;
    }
    calc_triclinic_images(box, img + 1);

    write_sto_conf(fn, "Images", &atoms, img, NULL, ePBC, box);

    free_t_atoms(&atoms, FALSE);
    sfree(img);
}

void visualize_box(FILE *out, int a0, int r0, matrix box, rvec gridsize)
{
    int *edge;
    rvec *vert, shift;
    int nx, ny, nz, nbox, nat;
    int i, j, x, y, z;
    int rectedge[24] =
        { 0, 1, 1, 3, 3, 2, 0, 2, 0, 4, 1, 5, 3, 7, 2, 6, 4, 5, 5, 7, 7, 6, 6,
            4 };

    a0++;
    r0++;

    nx = (int) (gridsize[XX] + 0.5);
    ny = (int) (gridsize[YY] + 0.5);
    nz = (int) (gridsize[ZZ] + 0.5);
    nbox = nx * ny * nz;
    if (TRICLINIC(box))
    {
        nat = nbox * NCUCVERT;
        snew(vert,nat);
        calc_compact_unitcell_vertices(ecenterDEF, box, vert);
        j = 0;
        for (z = 0; z < nz; z++)
            for (y = 0; y < ny; y++)
                for (x = 0; x < nx; x++)
                {
                    for (i = 0; i < DIM; i++)
                        shift[i] = x * box[0][i] + y * box[1][i] + z
                            * box[2][i];
                    for (i = 0; i < NCUCVERT; i++)
                    {
                        rvec_add(vert[i], shift, vert[j]);
                        j++;
                    }
                }

        for (i = 0; i < nat; i++)
        {
            fprintf(out, pdbformat, "ATOM", a0 + i, "C", "BOX", 'K' + i
                / NCUCVERT, r0 + i, 10 * vert[i][XX], 10 * vert[i][YY], 10
                * vert[i][ZZ]);
            fprintf(out, "\n");
        }

        edge = compact_unitcell_edges();
        for (j = 0; j < nbox; j++)
            for (i = 0; i < NCUCEDGE; i++)
                fprintf(out, "CONECT%5d%5d\n", a0 + j * NCUCVERT + edge[2 * i],
                        a0 + j * NCUCVERT + edge[2 * i + 1]);

        sfree(vert);
    }
    else
    {
        i = 0;
        for (z = 0; z <= 1; z++)
            for (y = 0; y <= 1; y++)
                for (x = 0; x <= 1; x++)
                {
                    fprintf(out, pdbformat, "ATOM", a0 + i, "C", "BOX", 'K' + i
                        / 8, r0 + i, x * 10 * box[XX][XX],
                            y * 10 * box[YY][YY], z * 10 * box[ZZ][ZZ]);
                    fprintf(out, "\n");
                    i++;
                }
        for (i = 0; i < 24; i += 2)
            fprintf(out, "CONECT%5d%5d\n", a0 + rectedge[i], a0 + rectedge[i
                + 1]);
    }
}

void calc_rotmatrix(rvec principal_axis, rvec targetvec, matrix rotmatrix)
{
	rvec rotvec;
	real ux,uy,uz,costheta,sintheta;
	
	costheta = cos_angle(principal_axis,targetvec);
	sintheta=sqrt(1.0-costheta*costheta); /* sign is always positive since 0<theta<pi */
                
	/* Determine rotation from cross product with target vector */
	cprod(principal_axis,targetvec,rotvec);
	unitv(rotvec,rotvec);
	printf("Aligning %g %g %g to %g %g %g : xprod  %g %g %g\n",
		principal_axis[XX],principal_axis[YY],principal_axis[ZZ],targetvec[XX],targetvec[YY],targetvec[ZZ],
		rotvec[XX],rotvec[YY],rotvec[ZZ]);
		
	ux=rotvec[XX]; 
	uy=rotvec[YY]; 
	uz=rotvec[ZZ]; 
	rotmatrix[0][0]=ux*ux + (1.0-ux*ux)*costheta;
	rotmatrix[0][1]=ux*uy*(1-costheta)-uz*sintheta;
	rotmatrix[0][2]=ux*uz*(1-costheta)+uy*sintheta;
	rotmatrix[1][0]=ux*uy*(1-costheta)+uz*sintheta;
	rotmatrix[1][1]=uy*uy + (1.0-uy*uy)*costheta;
	rotmatrix[1][2]=uy*uz*(1-costheta)-ux*sintheta;
	rotmatrix[2][0]=ux*uz*(1-costheta)-uy*sintheta;
	rotmatrix[2][1]=uy*uz*(1-costheta)+ux*sintheta;
	rotmatrix[2][2]=uz*uz + (1.0-uz*uz)*costheta;
	
	printf("Rotation matrix: \n%g %g %g\n%g %g %g\n%g %g %g\n",
		rotmatrix[0][0],rotmatrix[0][1],rotmatrix[0][2],
		rotmatrix[1][0],rotmatrix[1][1],rotmatrix[1][2],
		rotmatrix[2][0],rotmatrix[2][1],rotmatrix[2][2]);
}

static void renum_resnr(t_atoms *atoms,int isize,const int *index,
                        int resnr_start)
{
    int i,resind_prev,resind;

    resind_prev = -1;
    for(i=0; i<isize; i++)
    {
        resind = atoms->atom[index == NULL ? i : index[i]].resind;
        if (resind != resind_prev)
        {
            atoms->resinfo[resind].nr = resnr_start;
            resnr_start++;
        }
        resind_prev = resind;
    }
}

int gmx_editconf(int argc, char *argv[])
{
    const char
        *desc[] =
            {
                "[TT]editconf[tt] converts generic structure format to [TT].gro[tt], [TT].g96[tt]",
                "or [TT].pdb[tt].",
                "[PAR]",
                "The box can be modified with options [TT]-box[tt], [TT]-d[tt] and",
                "[TT]-angles[tt]. Both [TT]-box[tt] and [TT]-d[tt]",
                "will center the system in the box, unless [TT]-noc[tt] is used.",
                "[PAR]",
                "Option [TT]-bt[tt] determines the box type: [TT]triclinic[tt] is a",
                "triclinic box, [TT]cubic[tt] is a rectangular box with all sides equal",
                "[TT]dodecahedron[tt] represents a rhombic dodecahedron and",
                "[TT]octahedron[tt] is a truncated octahedron.",
                "The last two are special cases of a triclinic box.",
                "The length of the three box vectors of the truncated octahedron is the",
                "shortest distance between two opposite hexagons.",
                "The volume of a dodecahedron is 0.71 and that of a truncated octahedron",
                "is 0.77 of that of a cubic box with the same periodic image distance.",
                "[PAR]",
                "Option [TT]-box[tt] requires only",
                "one value for a cubic box, dodecahedron and a truncated octahedron.",
                "[PAR]",
                "With [TT]-d[tt] and a [TT]triclinic[tt] box the size of the system in the x, y",
                "and z directions is used. With [TT]-d[tt] and [TT]cubic[tt],",
                "[TT]dodecahedron[tt] or [TT]octahedron[tt] boxes, the dimensions are set",
                "to the diameter of the system (largest distance between atoms) plus twice",
                "the specified distance.",
                "[PAR]",
                "Option [TT]-angles[tt] is only meaningful with option [TT]-box[tt] and",
                "a triclinic box and can not be used with option [TT]-d[tt].",
                "[PAR]",
                "When [TT]-n[tt] or [TT]-ndef[tt] is set, a group",
                "can be selected for calculating the size and the geometric center,",
                "otherwise the whole system is used.",
                "[PAR]",
                "[TT]-rotate[tt] rotates the coordinates and velocities.",
                "[PAR]",
                "[TT]-princ[tt] aligns the principal axes of the system along the",
                "coordinate axes, with the longest axis aligned with the x axis. ",
                "This may allow you to decrease the box volume,",
                "but beware that molecules can rotate significantly in a nanosecond.",
                "[PAR]",
                "Scaling is applied before any of the other operations are",
                "performed. Boxes and coordinates can be scaled to give a certain density (option",
                "[TT]-density[tt]). Note that this may be inaccurate in case a gro",
                "file is given as input. A special feature of the scaling option, when the",
                "factor -1 is given in one dimension, one obtains a mirror image,",
                "mirrored in one of the planes. When one uses -1 in three dimensions, ",
                "a point-mirror image is obtained.[PAR]",
                "Groups are selected after all operations have been applied.[PAR]",
                "Periodicity can be removed in a crude manner.",
                "It is important that the box vectors at the bottom of your input file",
                "are correct when the periodicity is to be removed.",
                "[PAR]",
                "When writing [TT].pdb[tt] files, B-factors can be",
                "added with the [TT]-bf[tt] option. B-factors are read",
                "from a file with with following format: first line states number of",
                "entries in the file, next lines state an index",
                "followed by a B-factor. The B-factors will be attached per residue",
                "unless an index is larger than the number of residues or unless the",
                "[TT]-atom[tt] option is set. Obviously, any type of numeric data can",
                "be added instead of B-factors. [TT]-legend[tt] will produce",
                "a row of CA atoms with B-factors ranging from the minimum to the",
                "maximum value found, effectively making a legend for viewing.",
                "[PAR]",
                "With the option [TT]-mead[tt] a special [TT].pdb[tt] ([TT].pqr[tt])",
                "file for the MEAD electrostatics",
                "program (Poisson-Boltzmann solver) can be made. A further prerequisite",
                "is that the input file is a run input file.",
                "The B-factor field is then filled with the Van der Waals radius",
                "of the atoms while the occupancy field will hold the charge.",
                "[PAR]",
                "The option [TT]-grasp[tt] is similar, but it puts the charges in the B-factor",
                "and the radius in the occupancy.",
                "[PAR]",
                "Option [TT]-align[tt] allows alignment",
                "of the principal axis of a specified group against the given vector, ",
				"with an optional center of rotation specified by [TT]-aligncenter[tt].",
                "[PAR]",
                "Finally with option [TT]-label[tt], [TT]editconf[tt] can add a chain identifier",
                "to a [TT].pdb[tt] file, which can be useful for analysis with e.g. rasmol.",
                "[PAR]",
                "To convert a truncated octrahedron file produced by a package which uses",
                "a cubic box with the corners cut off (such as GROMOS), use:[BR]",
                "[TT]editconf -f in -rotate 0 45 35.264 -bt o -box veclen -o out[tt][BR]",
                "where [TT]veclen[tt] is the size of the cubic box times sqrt(3)/2." };
    const char *bugs[] =
        {
            "For complex molecules, the periodicity removal routine may break down, "
                "in that case you can use [TT]trjconv[tt]." };
    static real dist = 0.0, rbox = 0.0, to_diam = 0.0;
    static gmx_bool bNDEF = FALSE, bRMPBC = FALSE, bCenter = FALSE, bReadVDW =
        FALSE, bCONECT = FALSE;
    static gmx_bool peratom = FALSE, bLegend = FALSE, bOrient = FALSE, bMead =
        FALSE, bGrasp = FALSE, bSig56 = FALSE;
    static rvec scale =
        { 1, 1, 1 }, newbox =
        { 0, 0, 0 }, newang =
        { 90, 90, 90 };
    static real rho = 1000.0, rvdw = 0.12;
    static rvec center =
        { 0, 0, 0 }, translation =
        { 0, 0, 0 }, rotangles =
        { 0, 0, 0 }, aligncenter =
		{ 0, 0, 0 }, targetvec =
        { 0, 0, 0 };
    static const char *btype[] =
        { NULL, "triclinic", "cubic", "dodecahedron", "octahedron", NULL },
        *label = "A";
    static rvec visbox =
        { 0, 0, 0 };
    static int resnr_start = -1;
    t_pargs
        pa[] =
            {
                    { "-ndef", FALSE, etBOOL,
                        { &bNDEF }, "Choose output from default index groups" },
                    { "-visbox", FALSE, etRVEC,
                        { visbox },
                        "HIDDENVisualize a grid of boxes, -1 visualizes the 14 box images" },
                    { "-bt", FALSE, etENUM,
                        { btype }, "Box type for -box and -d" },
                    { "-box", FALSE, etRVEC,
                        { newbox }, "Box vector lengths (a,b,c)" },
                    { "-angles", FALSE, etRVEC,
                        { newang }, "Angles between the box vectors (bc,ac,ab)" },
                    { "-d", FALSE, etREAL,
                        { &dist }, "Distance between the solute and the box" },
                    { "-c", FALSE, etBOOL,
                        { &bCenter },
                        "Center molecule in box (implied by -box and -d)" },
                    { "-center", FALSE, etRVEC,
                        { center }, "Coordinates of geometrical center" },
                    { "-aligncenter", FALSE, etRVEC,
                        { aligncenter }, "Center of rotation for alignment" },
                    { "-align", FALSE, etRVEC,
                        { targetvec },
                        "Align to target vector" },
                    { "-translate", FALSE, etRVEC,
                        { translation }, "Translation" },
                    { "-rotate", FALSE, etRVEC,
                        { rotangles },
                        "Rotation around the X, Y and Z axes in degrees" },
                    { "-princ", FALSE, etBOOL,
                        { &bOrient },
                        "Orient molecule(s) along their principal axes" },
                    { "-scale", FALSE, etRVEC,
                        { scale }, "Scaling factor" },
                    { "-density", FALSE, etREAL,
                        { &rho },
                        "Density (g/L) of the output box achieved by scaling" },
                    { "-pbc", FALSE, etBOOL,
                        { &bRMPBC },
                        "Remove the periodicity (make molecule whole again)" },
                    { "-resnr", FALSE, etINT,
                        { &resnr_start },
                        " Renumber residues starting from resnr" },
                    { "-grasp", FALSE, etBOOL,
                        { &bGrasp },
                        "Store the charge of the atom in the B-factor field and the radius of the atom in the occupancy field" },
                    {
                        "-rvdw", FALSE, etREAL,
                         { &rvdw },
                        "Default Van der Waals radius (in nm) if one can not be found in the database or if no parameters are present in the topology file" },
                    { "-sig56", FALSE, etREAL,
                        { &bSig56 },
                        "Use rmin/2 (minimum in the Van der Waals potential) rather than sigma/2 " },
                    {
                        "-vdwread", FALSE, etBOOL,
                        { &bReadVDW },
                        "Read the Van der Waals radii from the file vdwradii.dat rather than computing the radii based on the force field" },
                    { "-atom", FALSE, etBOOL,
                        { &peratom }, "Force B-factor attachment per atom" },
                    { "-legend", FALSE, etBOOL,
                        { &bLegend }, "Make B-factor legend" },
                    { "-label", FALSE, etSTR,
                        { &label }, "Add chain label for all residues" },
                    {
                        "-conect", FALSE, etBOOL,
                        { &bCONECT },
                        "Add CONECT records to a [TT].pdb[tt] file when written. Can only be done when a topology is present" } };
#define NPA asize(pa)

    FILE *out;
    const char *infile, *outfile;
    char title[STRLEN];
    int outftp, inftp, natom, i, j, n_bfac, itype, ntype;
    double *bfac = NULL, c6, c12;
    int *bfac_nr = NULL;
    t_topology *top = NULL;
    t_atoms atoms;
    char *grpname, *sgrpname, *agrpname;
    int isize, ssize, tsize, asize;
    atom_id *index, *sindex, *tindex, *aindex;
    rvec *x, *v, gc, min, max, size;
    int ePBC;
    matrix box,rotmatrix,trans;
	rvec princd,tmpvec;
    gmx_bool bIndex, bSetSize, bSetAng, bCubic, bDist, bSetCenter, bAlign;
    gmx_bool bHaveV, bScale, bRho, bTranslate, bRotate, bCalcGeom, bCalcDiam;
    real xs, ys, zs, xcent, ycent, zcent, diam = 0, mass = 0, d, vdw;
    gmx_atomprop_t aps;
    gmx_conect conect;
    output_env_t oenv;
    t_filenm fnm[] =
        {
            { efSTX, "-f", NULL, ffREAD },
            { efNDX, "-n", NULL, ffOPTRD },
            { efSTO, NULL, NULL, ffOPTWR },
            { efPQR, "-mead", "mead", ffOPTWR },
            { efDAT, "-bf", "bfact", ffOPTRD } };
#define NFILE asize(fnm)

    CopyRight(stderr, argv[0]);
    parse_common_args(&argc, argv, PCA_CAN_VIEW, NFILE, fnm, NPA, pa,
                      asize(desc), desc, asize(bugs), bugs, &oenv);

    bIndex = opt2bSet("-n", NFILE, fnm) || bNDEF;
    bMead = opt2bSet("-mead", NFILE, fnm);
    bSetSize = opt2parg_bSet("-box", NPA, pa);
    bSetAng = opt2parg_bSet("-angles", NPA, pa);
    bSetCenter = opt2parg_bSet("-center", NPA, pa);
    bDist = opt2parg_bSet("-d", NPA, pa);
	bAlign = opt2parg_bSet("-align", NPA, pa);
    /* Only automatically turn on centering without -noc */
    if ((bDist || bSetSize || bSetCenter) && !opt2parg_bSet("-c", NPA, pa))
    {
        bCenter = TRUE;
    }
    bScale = opt2parg_bSet("-scale", NPA, pa);
    bRho = opt2parg_bSet("-density", NPA, pa);
    bTranslate = opt2parg_bSet("-translate", NPA, pa);
    bRotate = opt2parg_bSet("-rotate", NPA, pa);
    if (bScale && bRho)
        fprintf(stderr, "WARNING: setting -density overrides -scale\n");
    bScale = bScale || bRho;
    bCalcGeom = bCenter || bRotate || bOrient || bScale;
    bCalcDiam = btype[0][0] == 'c' || btype[0][0] == 'd' || btype[0][0] == 'o';

    infile = ftp2fn(efSTX, NFILE, fnm);
    if (bMead)
        outfile = ftp2fn(efPQR, NFILE, fnm);
    else
        outfile = ftp2fn(efSTO, NFILE, fnm);
    outftp = fn2ftp(outfile);
    inftp = fn2ftp(infile);

    aps = gmx_atomprop_init();

    if (bMead && bGrasp)
    {
        printf("Incompatible options -mead and -grasp. Turning off -grasp\n");
        bGrasp = FALSE;
    }
    if (bGrasp && (outftp != efPDB))
        gmx_fatal(FARGS, "Output file should be a .pdb file"
        " when using the -grasp option\n");
        if ((bMead || bGrasp) && !((fn2ftp(infile) == efTPR) ||
                (fn2ftp(infile) == efTPA) ||
                (fn2ftp(infile) == efTPB)))
        gmx_fatal(FARGS,"Input file should be a .tp[abr] file"
            " when using the -mead option\n");

        get_stx_coordnum(infile,&natom);
        init_t_atoms(&atoms,natom,TRUE);
        snew(x,natom);
        snew(v,natom);
        read_stx_conf(infile,title,&atoms,x,v,&ePBC,box);
        if (fn2ftp(infile) == efPDB)
        {
            get_pdb_atomnumber(&atoms,aps);
        }
        printf("Read %d atoms\n",atoms.nr);

        /* Get the element numbers if available in a pdb file */
        if (fn2ftp(infile) == efPDB)
        get_pdb_atomnumber(&atoms,aps);

        if (ePBC != epbcNONE)
        {
            real vol = det(box);
            printf("Volume: %g nm^3, corresponds to roughly %d electrons\n",
                vol,100*((int)(vol*4.5)));
        }

        if (bMead || bGrasp || bCONECT)
        top = read_top(infile,NULL);

        if (bMead || bGrasp)
        {
            if (atoms.nr != top->atoms.nr)
            gmx_fatal(FARGS,"Atom numbers don't match (%d vs. %d)",atoms.nr,top->atoms.nr);
        snew(atoms.pdbinfo,top->atoms.nr); 
        ntype = top->idef.atnr;
        for(i=0; (i<atoms.nr); i++) {
            /* Determine the Van der Waals radius from the force field */
            if (bReadVDW) {
                if (!gmx_atomprop_query(aps,epropVDW,
                                        *top->atoms.resinfo[top->atoms.atom[i].resind].name,
                                        *top->atoms.atomname[i],&vdw))
                    vdw = rvdw;
            }
            else {
                itype = top->atoms.atom[i].type;
                c12   = top->idef.iparams[itype*ntype+itype].lj.c12;
                c6    = top->idef.iparams[itype*ntype+itype].lj.c6;
                if ((c6 != 0) && (c12 != 0)) {
                    real sig6; 
                    if (bSig56)
                        sig6 = 2*c12/c6;
                    else
                        sig6 = c12/c6;
                    vdw   = 0.5*pow(sig6,1.0/6.0);
                }
                else
                    vdw = rvdw;
            }
            /* Factor of 10 for nm -> Angstroms */
            vdw *= 10;

            if (bMead) {
                atoms.pdbinfo[i].occup = top->atoms.atom[i].q;
                atoms.pdbinfo[i].bfac  = vdw;
            }
            else {
                atoms.pdbinfo[i].occup = vdw;
                atoms.pdbinfo[i].bfac  = top->atoms.atom[i].q;
            }
        }
    }
    bHaveV=FALSE;
    for (i=0; (i<natom) && !bHaveV; i++)
        for (j=0; (j<DIM) && !bHaveV; j++)
            bHaveV=bHaveV || (v[i][j]!=0);
    printf("%selocities found\n",bHaveV?"V":"No v");

    if (visbox[0] > 0) {
        if (bIndex)
            gmx_fatal(FARGS,"Sorry, can not visualize box with index groups");
        if (outftp != efPDB)
            gmx_fatal(FARGS,"Sorry, can only visualize box with a pdb file");
    } else if (visbox[0] == -1)
        visualize_images("images.pdb",ePBC,box);

    /* remove pbc */
    if (bRMPBC) 
        rm_gropbc(&atoms,x,box);

    if (bCalcGeom) {
        if (bIndex) {
            fprintf(stderr,"\nSelect a group for determining the system size:\n");
            get_index(&atoms,ftp2fn_null(efNDX,NFILE,fnm),
                      1,&ssize,&sindex,&sgrpname);
        } else {
            ssize = atoms.nr;
            sindex = NULL;
        }
        diam=calc_geom(ssize,sindex,x,gc,min,max,bCalcDiam);
        rvec_sub(max, min, size);
        printf("    system size :%7.3f%7.3f%7.3f (nm)\n",
               size[XX], size[YY], size[ZZ]);
        if (bCalcDiam)
            printf("    diameter    :%7.3f               (nm)\n",diam);
        printf("    center      :%7.3f%7.3f%7.3f (nm)\n", gc[XX], gc[YY], gc[ZZ]);
        printf("    box vectors :%7.3f%7.3f%7.3f (nm)\n", 
               norm(box[XX]), norm(box[YY]), norm(box[ZZ]));
        printf("    box angles  :%7.2f%7.2f%7.2f (degrees)\n",
               norm2(box[ZZ])==0 ? 0 :
        RAD2DEG*acos(cos_angle_no_table(box[YY],box[ZZ])),
        norm2(box[ZZ])==0 ? 0 :
        RAD2DEG*acos(cos_angle_no_table(box[XX],box[ZZ])),
        norm2(box[YY])==0 ? 0 :
        RAD2DEG*acos(cos_angle_no_table(box[XX],box[YY])));
        printf("    box volume  :%7.2f               (nm^3)\n",det(box));
    }

    if (bRho || bOrient || bAlign)
        mass = calc_mass(&atoms,!fn2bTPX(infile),aps);

    if (bOrient) {
        atom_id *index;
        char    *grpnames;

        /* Get a group for principal component analysis */
        fprintf(stderr,"\nSelect group for the determining the orientation\n");
        get_index(&atoms,ftp2fn_null(efNDX,NFILE,fnm),1,&isize,&index,&grpnames);

        /* Orient the principal axes along the coordinate axes */
        orient_princ(&atoms,isize,index,natom,x,bHaveV ? v : NULL, NULL);
        sfree(index);
        sfree(grpnames);
    }

    if ( bScale ) {
        /* scale coordinates and box */
        if (bRho) {
            /* Compute scaling constant */
            real vol,dens;

            vol = det(box);
            dens = (mass*AMU)/(vol*NANO*NANO*NANO);
            fprintf(stderr,"Volume  of input %g (nm^3)\n",vol);
            fprintf(stderr,"Mass    of input %g (a.m.u.)\n",mass);
            fprintf(stderr,"Density of input %g (g/l)\n",dens);
            if (vol==0 || mass==0)
                gmx_fatal(FARGS,"Cannot scale density with "
                          "zero mass (%g) or volume (%g)\n",mass,vol);

            scale[XX] = scale[YY] = scale[ZZ] = pow(dens/rho,1.0/3.0);
            fprintf(stderr,"Scaling all box vectors by %g\n",scale[XX]);
        }
        scale_conf(atoms.nr,x,box,scale);
    }

	if (bAlign) {
		if (bIndex) {
            fprintf(stderr,"\nSelect a group that you want to align:\n");
            get_index(&atoms,ftp2fn_null(efNDX,NFILE,fnm),
                      1,&asize,&aindex,&agrpname);
        } else {
            asize = atoms.nr;
            snew(aindex,asize);
			for (i=0;i<asize;i++)
				aindex[i]=i;
        }
		printf("Aligning %d atoms (out of %d) to %g %g %g, center of rotation %g %g %g\n",asize,natom,
			targetvec[XX],targetvec[YY],targetvec[ZZ],
			aligncenter[XX],aligncenter[YY],aligncenter[ZZ]);
		/*subtract out pivot point*/
		for(i=0; i<asize; i++)
			rvec_dec(x[aindex[i]],aligncenter);
		/*now determine transform and rotate*/
		/*will this work?*/
		principal_comp(asize,aindex,atoms.atom,x, trans,princd);

		unitv(targetvec,targetvec);
		printf("Using %g %g %g as principal axis\n", trans[0][2],trans[1][2],trans[2][2]);
		tmpvec[XX]=trans[0][2]; tmpvec[YY]=trans[1][2]; tmpvec[ZZ]=trans[2][2];
		calc_rotmatrix(tmpvec, targetvec, rotmatrix);
		/* rotmatrix finished */

		for (i=0;i<asize;++i)
		{
			mvmul(rotmatrix,x[aindex[i]],tmpvec);
			copy_rvec(tmpvec,x[aindex[i]]);
		}

		/*add pivot point back*/
		for(i=0; i<asize; i++)
			rvec_inc(x[aindex[i]],aligncenter);
		if (!bIndex)
			sfree(aindex);
	}

    if (bTranslate) {
        if (bIndex) {
            fprintf(stderr,"\nSelect a group that you want to translate:\n");
            get_index(&atoms,ftp2fn_null(efNDX,NFILE,fnm),
                      1,&ssize,&sindex,&sgrpname);
        } else {
            ssize = atoms.nr;
            sindex = NULL;
        }
        printf("Translating %d atoms (out of %d) by %g %g %g nm\n",ssize,natom,
               translation[XX],translation[YY],translation[ZZ]);
        if (sindex) {
            for(i=0; i<ssize; i++)
                rvec_inc(x[sindex[i]],translation);
        }
        else {
            for(i=0; i<natom; i++)
                rvec_inc(x[i],translation);
        }
    }
    if (bRotate) {
        /* Rotate */
        printf("Rotating %g, %g, %g degrees around the X, Y and Z axis respectively\n",rotangles[XX],rotangles[YY],rotangles[ZZ]);
        for(i=0; i<DIM; i++)
            rotangles[i] *= DEG2RAD;
        rotate_conf(natom,x,v,rotangles[XX],rotangles[YY],rotangles[ZZ]);
    }

    if (bCalcGeom) {
        /* recalc geometrical center and max and min coordinates and size */
        calc_geom(ssize,sindex,x,gc,min,max,FALSE);
        rvec_sub(max, min, size);
        if (bScale || bOrient || bRotate)
            printf("new system size : %6.3f %6.3f %6.3f\n",
                   size[XX],size[YY],size[ZZ]);
    }

    if (bSetSize || bDist || (btype[0][0]=='t' && bSetAng)) {
        ePBC = epbcXYZ;
        if (!(bSetSize || bDist))
            for (i=0; i<DIM; i++)
                newbox[i] = norm(box[i]);
        clear_mat(box);
        /* calculate new boxsize */
        switch(btype[0][0]){
        case 't':
            if (bDist)
                for(i=0; i<DIM; i++)
                    newbox[i] = size[i]+2*dist;
            if (!bSetAng) {
                box[XX][XX] = newbox[XX];
                box[YY][YY] = newbox[YY];
                box[ZZ][ZZ] = newbox[ZZ];
            } else {
                matrix_convert(box,newbox,newang);
            }
            break;
        case 'c':
        case 'd':
        case 'o':
            if (bSetSize)
                d = newbox[0];
            else
                d = diam+2*dist;
            if (btype[0][0] == 'c')
                for(i=0; i<DIM; i++)
                    box[i][i] = d;
            else if (btype[0][0] == 'd') {
                box[XX][XX] = d;
                box[YY][YY] = d;
                box[ZZ][XX] = d/2;
                box[ZZ][YY] = d/2;
                box[ZZ][ZZ] = d*sqrt(2)/2;
            } else {
                box[XX][XX] = d;
                box[YY][XX] = d/3;
                box[YY][YY] = d*sqrt(2)*2/3;
                box[ZZ][XX] = -d/3;
                box[ZZ][YY] = d*sqrt(2)/3;
                box[ZZ][ZZ] = d*sqrt(6)/3;
            }
            break;
        } 
    }

    /* calculate new coords for geometrical center */
    if (!bSetCenter)
        calc_box_center(ecenterDEF,box,center);

    /* center molecule on 'center' */
    if (bCenter)
        center_conf(natom,x,center,gc);

    /* print some */
    if (bCalcGeom) {
        calc_geom(ssize,sindex,x, gc, min, max, FALSE);
        printf("new center      :%7.3f%7.3f%7.3f (nm)\n",gc[XX],gc[YY],gc[ZZ]);
    }
    if (bOrient || bScale || bDist || bSetSize) {
        printf("new box vectors :%7.3f%7.3f%7.3f (nm)\n", 
               norm(box[XX]), norm(box[YY]), norm(box[ZZ]));
        printf("new box angles  :%7.2f%7.2f%7.2f (degrees)\n",
               norm2(box[ZZ])==0 ? 0 :
        RAD2DEG*acos(cos_angle_no_table(box[YY],box[ZZ])),
        norm2(box[ZZ])==0 ? 0 :
        RAD2DEG*acos(cos_angle_no_table(box[XX],box[ZZ])),
        norm2(box[YY])==0 ? 0 :
        RAD2DEG*acos(cos_angle_no_table(box[XX],box[YY])));
        printf("new box volume  :%7.2f               (nm^3)\n",det(box));
    }  

    if (check_box(epbcXYZ,box))
        printf("\nWARNING: %s\n",check_box(epbcXYZ,box));

    if (bDist && btype[0][0]=='t')
    {
        if(TRICLINIC(box))
        {
            printf("\nWARNING: Your box is triclinic with non-orthogonal axes. In this case, the\n"
                "distance from the solute to a box surface along the corresponding normal\n"
                "vector might be somewhat smaller than your specified value %f.\n"
                "You can check the actual value with g_mindist -pi\n",dist);
        }
        else if (!opt2parg_bSet("-bt", NPA, pa))
        {
            printf("\nWARNING: No boxtype specified - distance condition applied in each dimension.\n"
                "If the molecule rotates the actual distance will be smaller. You might want\n"
                "to use a cubic box instead, or why not try a dodecahedron today?\n");
        }
    }
    if (bCONECT && (outftp == efPDB) && (inftp == efTPR)) 
        conect = gmx_conect_generate(top);
    else
        conect = NULL;

    if (bIndex) {
        fprintf(stderr,"\nSelect a group for output:\n");
        get_index(&atoms,opt2fn_null("-n",NFILE,fnm),
                  1,&isize,&index,&grpname);

        if (resnr_start >= 0)
        {
            renum_resnr(&atoms,isize,index,resnr_start);
        }

        if (opt2parg_bSet("-label",NPA,pa)) {
            for(i=0; (i<atoms.nr); i++) 
                atoms.resinfo[atoms.atom[i].resind].chainid=label[0];
        }
                
        if (opt2bSet("-bf",NFILE,fnm) || bLegend)
        {
            gmx_fatal(FARGS,"Sorry, cannot do bfactors with an index group.");
        }

        if (outftp == efPDB) 
        {
            out=ffopen(outfile,"w");
            write_pdbfile_indexed(out,title,&atoms,x,ePBC,box,' ',1,isize,index,conect,TRUE);
            ffclose(out);
        }
        else
        {
            write_sto_conf_indexed(outfile,title,&atoms,x,bHaveV?v:NULL,ePBC,box,isize,index); 
        }
    }
    else
    {
        if (resnr_start >= 0)
        {
            renum_resnr(&atoms,atoms.nr,NULL,resnr_start);
        }

        if ((outftp == efPDB) || (outftp == efPQR)) {
            out=ffopen(outfile,"w");
            if (bMead) {
                set_pdb_wide_format(TRUE);
                fprintf(out,"REMARK    "
                        "The B-factors in this file hold atomic radii\n");
                fprintf(out,"REMARK    "
                        "The occupancy in this file hold atomic charges\n");
            }
            else if (bGrasp) {
                fprintf(out,"GRASP PDB FILE\nFORMAT NUMBER=1\n");
                fprintf(out,"REMARK    "
                        "The B-factors in this file hold atomic charges\n");
                fprintf(out,"REMARK    "
                        "The occupancy in this file hold atomic radii\n");
            }
            else if (opt2bSet("-bf",NFILE,fnm)) {
                read_bfac(opt2fn("-bf",NFILE,fnm),&n_bfac,&bfac,&bfac_nr);
                set_pdb_conf_bfac(atoms.nr,atoms.nres,&atoms,
                                  n_bfac,bfac,bfac_nr,peratom);
            }
            if (opt2parg_bSet("-label",NPA,pa)) {
                for(i=0; (i<atoms.nr); i++) 
                    atoms.resinfo[atoms.atom[i].resind].chainid=label[0];
            }
            write_pdbfile(out,title,&atoms,x,ePBC,box,' ',-1,conect,TRUE);
            if (bLegend)
                pdb_legend(out,atoms.nr,atoms.nres,&atoms,x);
            if (visbox[0] > 0)
                visualize_box(out,bLegend ? atoms.nr+12 : atoms.nr,
                    bLegend? atoms.nres=12 : atoms.nres,box,visbox);
            ffclose(out);
        }
        else
            write_sto_conf(outfile,title,&atoms,x,bHaveV?v:NULL,ePBC,box); 
    }
    gmx_atomprop_destroy(aps);

    do_view(oenv,outfile,NULL);

    thanx(stderr);

    return 0;
}
